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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include <algorithm> |
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#include <math.h> |
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#include "primitives/RigidBody.hpp" |
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#include "utils/simError.h" |
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#include "utils/NumericConstant.hpp" |
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namespace OpenMD { |
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|
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RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), |
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inertiaTensor_(0.0){ |
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} |
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|
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void RigidBody::setPrevA(const RotMat3x3d& a) { |
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((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
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|
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for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
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if (atoms_[i]->isDirectional()) { |
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atoms_[i]->setPrevA(refOrients_[i].transpose() * a); |
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} |
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} |
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|
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} |
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|
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|
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void RigidBody::setA(const RotMat3x3d& a) { |
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((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
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|
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for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
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if (atoms_[i]->isDirectional()) { |
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atoms_[i]->setA(refOrients_[i].transpose() * a); |
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} |
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} |
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} |
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|
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void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) { |
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((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
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|
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for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
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if (atoms_[i]->isDirectional()) { |
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atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo); |
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} |
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} |
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|
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} |
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|
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Mat3x3d RigidBody::getI() { |
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return inertiaTensor_; |
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} |
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|
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std::vector<RealType> RigidBody::getGrad() { |
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std::vector<RealType> grad(6, 0.0); |
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Vector3d force; |
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Vector3d torque; |
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Vector3d myEuler; |
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RealType phi, theta; |
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// RealType psi; |
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RealType cphi, sphi, ctheta, stheta; |
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Vector3d ephi; |
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Vector3d etheta; |
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Vector3d epsi; |
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|
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force = getFrc(); |
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torque =getTrq(); |
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myEuler = getA().toEulerAngles(); |
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|
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phi = myEuler[0]; |
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theta = myEuler[1]; |
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// psi = myEuler[2]; |
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|
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cphi = cos(phi); |
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sphi = sin(phi); |
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ctheta = cos(theta); |
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stheta = sin(theta); |
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|
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// get unit vectors along the phi, theta and psi rotation axes |
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|
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ephi[0] = 0.0; |
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ephi[1] = 0.0; |
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ephi[2] = 1.0; |
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|
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//etheta[0] = -sphi; |
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//etheta[1] = cphi; |
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//etheta[2] = 0.0; |
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|
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etheta[0] = cphi; |
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etheta[1] = sphi; |
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etheta[2] = 0.0; |
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|
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epsi[0] = stheta * cphi; |
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epsi[1] = stheta * sphi; |
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epsi[2] = ctheta; |
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|
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//gradient is equal to -force |
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for (int j = 0 ; j<3; j++) |
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grad[j] = -force[j]; |
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|
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for (int j = 0; j < 3; j++ ) { |
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|
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grad[3] += torque[j]*ephi[j]; |
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grad[4] += torque[j]*etheta[j]; |
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grad[5] += torque[j]*epsi[j]; |
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|
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} |
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|
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return grad; |
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} |
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|
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void RigidBody::accept(BaseVisitor* v) { |
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v->visit(this); |
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} |
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|
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/**@todo need modification */ |
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void RigidBody::calcRefCoords() { |
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RealType mtmp; |
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Vector3d refCOM(0.0); |
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mass_ = 0.0; |
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for (std::size_t i = 0; i < atoms_.size(); ++i) { |
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mtmp = atoms_[i]->getMass(); |
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mass_ += mtmp; |
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refCOM += refCoords_[i]*mtmp; |
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} |
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refCOM /= mass_; |
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|
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// Next, move the origin of the reference coordinate system to the COM: |
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for (std::size_t i = 0; i < atoms_.size(); ++i) { |
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refCoords_[i] -= refCOM; |
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} |
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|
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// Moment of Inertia calculation |
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Mat3x3d Itmp(0.0); |
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for (std::size_t i = 0; i < atoms_.size(); i++) { |
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Mat3x3d IAtom(0.0); |
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mtmp = atoms_[i]->getMass(); |
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IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp; |
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RealType r2 = refCoords_[i].lengthSquare(); |
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IAtom(0, 0) += mtmp * r2; |
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IAtom(1, 1) += mtmp * r2; |
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IAtom(2, 2) += mtmp * r2; |
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Itmp += IAtom; |
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|
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//project the inertial moment of directional atoms into this rigid body |
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if (atoms_[i]->isDirectional()) { |
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Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i]; |
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} |
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} |
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|
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// std::cout << Itmp << std::endl; |
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|
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//diagonalize |
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Vector3d evals; |
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Mat3x3d::diagonalize(Itmp, evals, sU_); |
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|
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// zero out I and then fill the diagonals with the moments of inertia: |
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inertiaTensor_(0, 0) = evals[0]; |
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inertiaTensor_(1, 1) = evals[1]; |
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inertiaTensor_(2, 2) = evals[2]; |
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|
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int nLinearAxis = 0; |
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for (int i = 0; i < 3; i++) { |
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if (fabs(evals[i]) < OpenMD::epsilon) { |
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linear_ = true; |
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linearAxis_ = i; |
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++ nLinearAxis; |
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} |
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} |
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|
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if (nLinearAxis > 1) { |
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sprintf( painCave.errMsg, |
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"RigidBody error.\n" |
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"\tOpenMD found more than one axis in this rigid body with a vanishing \n" |
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"\tmoment of inertia. This can happen in one of three ways:\n" |
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"\t 1) Only one atom was specified, or \n" |
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"\t 2) All atoms were specified at the same location, or\n" |
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"\t 3) The programmers did something stupid.\n" |
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"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n" |
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); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} |
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|
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void RigidBody::calcForcesAndTorques() { |
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Vector3d afrc; |
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Vector3d atrq; |
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Vector3d apos; |
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Vector3d rpos; |
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Vector3d frc(0.0); |
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Vector3d trq(0.0); |
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Vector3d ef(0.0); |
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Vector3d pos = this->getPos(); |
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AtomType* atype; |
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int eCount = 0; |
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|
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int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout(); |
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|
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for (unsigned int i = 0; i < atoms_.size(); i++) { |
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|
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atype = atoms_[i]->getAtomType(); |
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|
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afrc = atoms_[i]->getFrc(); |
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apos = atoms_[i]->getPos(); |
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rpos = apos - pos; |
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|
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frc += afrc; |
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|
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trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
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trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
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trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
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|
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// If the atom has a torque associated with it, then we also need to |
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// migrate the torques onto the center of mass: |
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|
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if (atoms_[i]->isDirectional()) { |
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atrq = atoms_[i]->getTrq(); |
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trq += atrq; |
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} |
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|
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if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) { |
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ef += atoms_[i]->getElectricField(); |
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eCount++; |
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} |
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} |
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addFrc(frc); |
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addTrq(trq); |
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|
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if (sl & DataStorage::dslElectricField) { |
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ef /= eCount; |
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setElectricField(ef); |
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} |
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|
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} |
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|
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Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() { |
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Vector3d afrc; |
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Vector3d atrq; |
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Vector3d apos; |
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Vector3d rpos; |
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Vector3d dfrc; |
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Vector3d frc(0.0); |
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Vector3d trq(0.0); |
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Vector3d ef(0.0); |
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AtomType* atype; |
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int eCount = 0; |
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|
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Vector3d pos = this->getPos(); |
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Mat3x3d tau_(0.0); |
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|
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int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout(); |
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|
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for (unsigned int i = 0; i < atoms_.size(); i++) { |
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|
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atype = atoms_[i]->getAtomType(); |
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|
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afrc = atoms_[i]->getFrc(); |
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apos = atoms_[i]->getPos(); |
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rpos = apos - pos; |
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|
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frc += afrc; |
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|
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trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
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trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
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trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
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|
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// If the atom has a torque associated with it, then we also need to |
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// migrate the torques onto the center of mass: |
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|
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if (atoms_[i]->isDirectional()) { |
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atrq = atoms_[i]->getTrq(); |
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trq += atrq; |
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} |
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|
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if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) { |
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ef += atoms_[i]->getElectricField(); |
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eCount++; |
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} |
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|
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tau_(0,0) -= rpos[0]*afrc[0]; |
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tau_(0,1) -= rpos[0]*afrc[1]; |
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tau_(0,2) -= rpos[0]*afrc[2]; |
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tau_(1,0) -= rpos[1]*afrc[0]; |
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tau_(1,1) -= rpos[1]*afrc[1]; |
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tau_(1,2) -= rpos[1]*afrc[2]; |
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tau_(2,0) -= rpos[2]*afrc[0]; |
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tau_(2,1) -= rpos[2]*afrc[1]; |
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tau_(2,2) -= rpos[2]*afrc[2]; |
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|
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} |
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addFrc(frc); |
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addTrq(trq); |
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|
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if (sl & DataStorage::dslElectricField) { |
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ef /= eCount; |
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setElectricField(ef); |
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} |
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|
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return tau_; |
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} |
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|
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void RigidBody::updateAtoms() { |
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unsigned int i; |
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Vector3d ref; |
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Vector3d apos; |
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DirectionalAtom* dAtom; |
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Vector3d pos = getPos(); |
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RotMat3x3d a = getA(); |
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|
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for (i = 0; i < atoms_.size(); i++) { |
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|
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ref = body2Lab(refCoords_[i]); |
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|
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apos = pos + ref; |
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|
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atoms_[i]->setPos(apos); |
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|
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if (atoms_[i]->isDirectional()) { |
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|
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dAtom = dynamic_cast<DirectionalAtom *>(atoms_[i]); |
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dAtom->setA(refOrients_[i].transpose() * a); |
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} |
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|
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} |
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|
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} |
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|
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|
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void RigidBody::updateAtoms(int frame) { |
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unsigned int i; |
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Vector3d ref; |
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Vector3d apos; |
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DirectionalAtom* dAtom; |
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Vector3d pos = getPos(frame); |
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RotMat3x3d a = getA(frame); |
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|
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for (i = 0; i < atoms_.size(); i++) { |
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|
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ref = body2Lab(refCoords_[i], frame); |
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|
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apos = pos + ref; |
| 380 |
|
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atoms_[i]->setPos(apos, frame); |
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|
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if (atoms_[i]->isDirectional()) { |
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|
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dAtom = dynamic_cast<DirectionalAtom *>(atoms_[i]); |
| 386 |
dAtom->setA(refOrients_[i].transpose() * a, frame); |
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} |
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|
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} |
| 390 |
|
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} |
| 392 |
|
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void RigidBody::updateAtomVel() { |
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Mat3x3d skewMat; |
| 395 |
|
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Vector3d ji = getJ(); |
| 397 |
Mat3x3d I = getI(); |
| 398 |
|
| 399 |
skewMat(0, 0) =0; |
| 400 |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 401 |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 402 |
|
| 403 |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 404 |
skewMat(1, 1) = 0; |
| 405 |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 406 |
|
| 407 |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 408 |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 409 |
skewMat(2, 2) = 0; |
| 410 |
|
| 411 |
Mat3x3d mat = (getA() * skewMat).transpose(); |
| 412 |
Vector3d rbVel = getVel(); |
| 413 |
|
| 414 |
|
| 415 |
Vector3d velRot; |
| 416 |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 417 |
atoms_[i]->setVel(rbVel + mat * refCoords_[i]); |
| 418 |
} |
| 419 |
|
| 420 |
} |
| 421 |
|
| 422 |
void RigidBody::updateAtomVel(int frame) { |
| 423 |
Mat3x3d skewMat;; |
| 424 |
|
| 425 |
Vector3d ji = getJ(frame); |
| 426 |
Mat3x3d I = getI(); |
| 427 |
|
| 428 |
skewMat(0, 0) =0; |
| 429 |
skewMat(0, 1) = ji[2] /I(2, 2); |
| 430 |
skewMat(0, 2) = -ji[1] /I(1, 1); |
| 431 |
|
| 432 |
skewMat(1, 0) = -ji[2] /I(2, 2); |
| 433 |
skewMat(1, 1) = 0; |
| 434 |
skewMat(1, 2) = ji[0]/I(0, 0); |
| 435 |
|
| 436 |
skewMat(2, 0) =ji[1] /I(1, 1); |
| 437 |
skewMat(2, 1) = -ji[0]/I(0, 0); |
| 438 |
skewMat(2, 2) = 0; |
| 439 |
|
| 440 |
Mat3x3d mat = (getA(frame) * skewMat).transpose(); |
| 441 |
Vector3d rbVel = getVel(frame); |
| 442 |
|
| 443 |
|
| 444 |
Vector3d velRot; |
| 445 |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 446 |
atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame); |
| 447 |
} |
| 448 |
|
| 449 |
} |
| 450 |
|
| 451 |
|
| 452 |
|
| 453 |
bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) { |
| 454 |
if (index < atoms_.size()) { |
| 455 |
|
| 456 |
Vector3d ref = body2Lab(refCoords_[index]); |
| 457 |
pos = getPos() + ref; |
| 458 |
return true; |
| 459 |
} else { |
| 460 |
std::cerr << index << " is an invalid index, current rigid body contains " |
| 461 |
<< atoms_.size() << "atoms" << std::endl; |
| 462 |
return false; |
| 463 |
} |
| 464 |
} |
| 465 |
|
| 466 |
bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) { |
| 467 |
std::vector<Atom*>::iterator i; |
| 468 |
i = std::find(atoms_.begin(), atoms_.end(), atom); |
| 469 |
if (i != atoms_.end()) { |
| 470 |
//RigidBody class makes sure refCoords_ and atoms_ match each other |
| 471 |
Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]); |
| 472 |
pos = getPos() + ref; |
| 473 |
return true; |
| 474 |
} else { |
| 475 |
std::cerr << "Atom " << atom->getGlobalIndex() |
| 476 |
<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
| 477 |
return false; |
| 478 |
} |
| 479 |
} |
| 480 |
bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) { |
| 481 |
|
| 482 |
//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$ |
| 483 |
|
| 484 |
if (index < atoms_.size()) { |
| 485 |
|
| 486 |
Vector3d velRot; |
| 487 |
Mat3x3d skewMat;; |
| 488 |
Vector3d ref = refCoords_[index]; |
| 489 |
Vector3d ji = getJ(); |
| 490 |
Mat3x3d I = getI(); |
| 491 |
|
| 492 |
skewMat(0, 0) = 0; |
| 493 |
skewMat(0, 1) = ji[2] / I(2, 2); |
| 494 |
skewMat(0, 2) = -ji[1] / I(1, 1); |
| 495 |
|
| 496 |
skewMat(1, 0) = -ji[2] / I(2, 2); |
| 497 |
skewMat(1, 1) = 0; |
| 498 |
skewMat(1, 2) = ji[0]/ I(0, 0); |
| 499 |
|
| 500 |
skewMat(2, 0) = ji[1] / I(1, 1); |
| 501 |
skewMat(2, 1) = -ji[0] / I(0, 0); |
| 502 |
skewMat(2, 2) = 0; |
| 503 |
|
| 504 |
velRot = (getA() * skewMat).transpose() * ref; |
| 505 |
|
| 506 |
vel = getVel() + velRot; |
| 507 |
return true; |
| 508 |
|
| 509 |
} else { |
| 510 |
std::cerr << index |
| 511 |
<< " is an invalid index, current rigid body contains " |
| 512 |
<< atoms_.size() << "atoms" << std::endl; |
| 513 |
return false; |
| 514 |
} |
| 515 |
} |
| 516 |
|
| 517 |
bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) { |
| 518 |
|
| 519 |
std::vector<Atom*>::iterator i; |
| 520 |
i = std::find(atoms_.begin(), atoms_.end(), atom); |
| 521 |
if (i != atoms_.end()) { |
| 522 |
return getAtomVel(vel, i - atoms_.begin()); |
| 523 |
} else { |
| 524 |
std::cerr << "Atom " << atom->getGlobalIndex() |
| 525 |
<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
| 526 |
return false; |
| 527 |
} |
| 528 |
} |
| 529 |
|
| 530 |
bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) { |
| 531 |
if (index < atoms_.size()) { |
| 532 |
|
| 533 |
coor = refCoords_[index]; |
| 534 |
return true; |
| 535 |
} else { |
| 536 |
std::cerr << index << " is an invalid index, current rigid body contains " |
| 537 |
<< atoms_.size() << "atoms" << std::endl; |
| 538 |
return false; |
| 539 |
} |
| 540 |
|
| 541 |
} |
| 542 |
|
| 543 |
bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) { |
| 544 |
std::vector<Atom*>::iterator i; |
| 545 |
i = std::find(atoms_.begin(), atoms_.end(), atom); |
| 546 |
if (i != atoms_.end()) { |
| 547 |
//RigidBody class makes sure refCoords_ and atoms_ match each other |
| 548 |
coor = refCoords_[i - atoms_.begin()]; |
| 549 |
return true; |
| 550 |
} else { |
| 551 |
std::cerr << "Atom " << atom->getGlobalIndex() |
| 552 |
<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl; |
| 553 |
return false; |
| 554 |
} |
| 555 |
|
| 556 |
} |
| 557 |
|
| 558 |
|
| 559 |
void RigidBody::addAtom(Atom* at, AtomStamp* ats) { |
| 560 |
|
| 561 |
Vector3d coords; |
| 562 |
Vector3d euler; |
| 563 |
|
| 564 |
|
| 565 |
atoms_.push_back(at); |
| 566 |
|
| 567 |
if( !ats->havePosition() ){ |
| 568 |
sprintf( painCave.errMsg, |
| 569 |
"RigidBody error.\n" |
| 570 |
"\tAtom %s does not have a position specified.\n" |
| 571 |
"\tThis means RigidBody cannot set up reference coordinates.\n", |
| 572 |
ats->getType().c_str() ); |
| 573 |
painCave.isFatal = 1; |
| 574 |
simError(); |
| 575 |
} |
| 576 |
|
| 577 |
coords[0] = ats->getPosX(); |
| 578 |
coords[1] = ats->getPosY(); |
| 579 |
coords[2] = ats->getPosZ(); |
| 580 |
|
| 581 |
refCoords_.push_back(coords); |
| 582 |
|
| 583 |
RotMat3x3d identMat = RotMat3x3d::identity(); |
| 584 |
|
| 585 |
if (at->isDirectional()) { |
| 586 |
|
| 587 |
if( !ats->haveOrientation() ){ |
| 588 |
sprintf( painCave.errMsg, |
| 589 |
"RigidBody error.\n" |
| 590 |
"\tAtom %s does not have an orientation specified.\n" |
| 591 |
"\tThis means RigidBody cannot set up reference orientations.\n", |
| 592 |
ats->getType().c_str() ); |
| 593 |
painCave.isFatal = 1; |
| 594 |
simError(); |
| 595 |
} |
| 596 |
|
| 597 |
euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0; |
| 598 |
euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0; |
| 599 |
euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0; |
| 600 |
|
| 601 |
RotMat3x3d Atmp(euler); |
| 602 |
refOrients_.push_back(Atmp); |
| 603 |
|
| 604 |
}else { |
| 605 |
refOrients_.push_back(identMat); |
| 606 |
} |
| 607 |
|
| 608 |
|
| 609 |
} |
| 610 |
|
| 611 |
} |
| 612 |
|
